Exactly--people were happy with the old UI, which, non-standard or not, was in place for ~ a decade. They really resented having to learn something new. Now repeat that experience once for every new application you want to use. It can be extremely frustrating.
The point is that "UI nativity" means things like "checkmarks in checkboxes should appear in the same way across all applications". It's pretty easy to distinguish a checkmark in a checkbox no matter what platform you're on, and real users don't care if it matches the rest of the platform exactly or not.
"UI nativity" is basically a way for design snobs to feel like they're making a contribution by whining about something trivial and irrelevant. A normal person can still recognize the meaning and doesn't care if the checkbox is beveled differently from app to app, and anyone who discards an application on such minor inconsistencies is not doing serious work anyway, and should be disregarded.
